The Brooklyn-Battery Tunnel became one of the city's most dramatic sights during Hurricane Sandy, as the storm sent 90 million gallons of New York Harbor water rushing into the tube, filling it completely.

But for at least one major New York landlord, the fact that the tunnel was positioned to take on all that water turned out to be something of a blessing.

"I had one very prominent real estate builder who owns buildings in lower Manhattan—actually all over the city—thank me for allowing the Brooklyn-Battery tunnel to be used as a drainage ditch," M.T.A. chairman Joe Lhota told me recently. "I wasn’t particularly pleased with the comment.”

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(Lhota confirmed during our conversation that he was referring to Bill Rudin.)

The M.T.A. has recently begun to float different ideas for protecting the system's tunnels in the future from flooding during such storms, which are expected to increase in frequency as the climate warms. Industrial balloons and flood gates are among the ideas under discussion.

"The fact of the matter is, if I plug it up, we plug it up, the M.T.A. plugs it up—if God forbid this happens again, the surge is the same or even higher, the water will go elsewhere," said Lhota.

And elsewhere could include the lower floors of nearby buildings, like those owned by Rudin Management at One Battery Park Plaza and One Whitehall Street.

Rudin, the scion of a storied New York real estate family and chairman of the influential Association for a Better New York, declined comment.

But his larger point, as recounted by Lhota, is a "plausible one," says Elliott Sclar, an urban planning professor at Columbia University.

"I think the bigger issue that he's raising here is that we have to think about lower Manhattan a lot more systemically, because a lot of it is landfill and it really is going to be the weak link in the chain," said Sclar.

In order to prevent future storm surges from wreaking similar havoc downtown, there's going to have to be better protection against flooding, but also better drainage.

"The Brooklyn-Battery Tunnel is probably one of those places where if it was possible to harden some of the infrastructure ... in such a way that it could flood without sustaining huge amounts of damage, it could be useful," said Richard Barone, the director of transportation programs at the Regional Plan Association.

He added, "The idea of letting things flood versus waterproofing them are options we have to consider."

UPDATE: A spokesperson for Rudin sends the following statement: "For almost a century, my family has been invested in the future of all parts of New York City. As we look post-Hurricane Sandy to New York’s long-term recovery, we have to consider a variety of options to effectively protect and defend our critical infrastructure as well as our residents, businesses and visitors. The public and the private sectors are actively involved and collaborating to come up with solutions to ensure that the City’s infrastructure and buildings are resilient in today’s unpredictable climate."

UPDATE: Lhota adds the following: “Bill Rudin is one of New York City’s most ardent champions, and the Rudin Family has long been at the forefront advocating for the city’s future and for all New Yorkers. Bill and I witnessed the horrific damage of Superstorm Sandy and we both concluded that we must have a comprehensive effort by the federal, state and local governments and the private sector to prevent such water surge damage to property in the future. I have no doubt that Bill will be an exemplary leader of this effort.”